AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1447590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1447590 MtrunA17_Chr8g0390941 92.523 214 13 1 1 214 1 211 6.63e-141 392
Msa1447590 MtrunA17_Chr6g0484631 39.749 239 108 10 3 214 2 231 1.15e-35 125
Msa1447590 MtrunA17_Chr1g0209961 35.882 170 86 9 60 213 102 264 6.49e-13 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1447590 AT1G13360.1 36.686 169 91 6 56 213 30 193 1.03e-18 80.9
Msa1447590 AT1G13360.2 33.333 162 95 5 56 211 30 184 2.39e-13 66.2
Msa1447590 AT1G13360.3 34.247 146 85 4 56 195 30 170 1.61e-12 63.9

Find 61 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATTTAAGCGGGTTCTTT+TGG 0.272845 tig0031918:-40826 Msa1447590:CDS
CAATGAAGCGTTTGGTTTCA+TGG 0.307425 tig0031918:-40783 Msa1447590:CDS
CCTCGTTTGGCGTCACCGTC+GGG 0.327008 tig0031918:+40900 None:intergenic
CGACCCGAATCGTTGGTTTC+AGG 0.353831 tig0031918:+40866 None:intergenic
ATCGTCACGAACTCGTTTCC+TGG 0.355014 tig0031918:+41267 None:intergenic
TCCAATAGATATCCTAGGTT+CGG 0.356990 tig0031918:+40950 None:intergenic
CCCGAACCTAGGATATCTAT+TGG 0.367430 tig0031918:-40951 Msa1447590:CDS
GTGGAGGTCGGAGACGTTGC+AGG 0.375651 tig0031918:-40675 Msa1447590:CDS
CCAATAGATATCCTAGGTTC+GGG 0.386519 tig0031918:+40951 None:intergenic
TCCTCGTTTGGCGTCACCGT+CGG 0.397307 tig0031918:+40899 None:intergenic
ATTCGTAACAATGAAGCGTT+TGG 0.420261 tig0031918:-40791 Msa1447590:CDS
TGAAGACGAAATACTTGCTC+CGG 0.429950 tig0031918:-41020 Msa1447590:CDS
GAATCGGTTTCAACTTGAAC+GGG 0.432240 tig0031918:+41142 None:intergenic
CCGCTTAAATCAACTCCATC+TGG 0.440348 tig0031918:+40836 None:intergenic
AATGAAGCGTTTGGTTTCAT+GGG 0.449168 tig0031918:-40782 Msa1447590:CDS
GTTGCCTGAAACCAACGATT+CGG 0.458751 tig0031918:-40870 Msa1447590:CDS
AGTTGAAACCGATTCGTATG+AGG 0.466901 tig0031918:-41134 Msa1447590:CDS
TTGCCTGAAACCAACGATTC+GGG 0.467717 tig0031918:-40869 Msa1447590:CDS
CTCGTTAACCTCATACGAAT+CGG 0.483054 tig0031918:+41126 None:intergenic
GGCGGTTATGTAACAATTGA+CGG 0.496161 tig0031918:-40731 Msa1447590:CDS
GGACGAGTTATCATCGGAAC+CGG 0.496783 tig0031918:+41195 None:intergenic
TCGGGTCGGGTTGGTCCAGA+TGG 0.500003 tig0031918:-40851 Msa1447590:CDS
TGAAACCAACGATTCGGGTC+GGG 0.501948 tig0031918:-40864 Msa1447590:CDS
GGGTTTAAATCGTCAGAGAC+TGG 0.503260 tig0031918:+40971 None:intergenic
CAGAGACTGGTACATGGGTC+GGG 0.513316 tig0031918:+40984 None:intergenic
GAAGCTTCTGATGATGAACT+TGG 0.514415 tig0031918:-40929 Msa1447590:CDS
CAGATGGAGTTGATTTAAGC+GGG 0.517002 tig0031918:-40835 Msa1447590:CDS
CGAGTTCTCCGAGTTGACTC+CGG 0.521332 tig0031918:-41214 Msa1447590:CDS
AGAAAATGTCACCACCGTGC+AGG 0.523129 tig0031918:-41068 Msa1447590:CDS
GCCACCATTGTCGTCGGCGA+CGG 0.524000 tig0031918:+40751 None:intergenic
CATCGGAACCGGAGTCAACT+CGG 0.524800 tig0031918:+41206 None:intergenic
GCTCGTGTGTTGACTCAGAC+GGG 0.533313 tig0031918:-41171 Msa1447590:CDS
CGAATCGGTTTCAACTTGAA+CGG 0.535630 tig0031918:+41141 None:intergenic
CTCGTTTGGCGTCACCGTCG+GGG 0.537489 tig0031918:+40901 None:intergenic
GGCTCGTGTGTTGACTCAGA+CGG 0.537857 tig0031918:-41172 Msa1447590:CDS
AAGCTTCCAATAGATATCCT+AGG 0.540677 tig0031918:+40945 None:intergenic
TCAGAGACTGGTACATGGGT+CGG 0.547147 tig0031918:+40983 None:intergenic
GAAGACGAAATACTTGCTCC+GGG 0.549263 tig0031918:-41019 Msa1447590:CDS
ATCGTCAGAGACTGGTACAT+GGG 0.558936 tig0031918:+40979 None:intergenic
GTCGCCGACGACAATGGTGG+CGG 0.560649 tig0031918:-40749 Msa1447590:CDS
AATCGTCAGAGACTGGTACA+TGG 0.570580 tig0031918:+40978 None:intergenic
GTCTGAGTCAACACACGAGC+CGG 0.573783 tig0031918:+41174 None:intergenic
ACCAACCCGACCCGAATCGT+TGG 0.573847 tig0031918:+40859 None:intergenic
GAAAATGTCACCACCGTGCA+GGG 0.573945 tig0031918:-41067 Msa1447590:CDS
CTGAAACCAACGATTCGGGT+CGG 0.591166 tig0031918:-40865 Msa1447590:CDS
GGTTCCGATGATAACTCGTC+CGG 0.592036 tig0031918:-41193 Msa1447590:CDS
CTGTTTGATTATGCTGACTC+CGG 0.597147 tig0031918:-40707 Msa1447590:CDS
CCAGATGGAGTTGATTTAAG+CGG 0.597918 tig0031918:-40836 Msa1447590:CDS
TCGTTTGGCGTCACCGTCGG+GGG 0.599566 tig0031918:+40902 None:intergenic
GACGCCGTCGCCGACGACAA+TGG 0.606214 tig0031918:-40755 Msa1447590:CDS
CGACCTCCACAAAAGATCAC+CGG 0.608830 tig0031918:+40688 None:intergenic
ACCAACGATTCGGGTCGGGT+TGG 0.616280 tig0031918:-40860 Msa1447590:CDS
GCCGTCGCCGACGACAATGG+TGG 0.616354 tig0031918:-40752 Msa1447590:CDS
GTCGGGTTCAAATCTTGACC+CGG 0.617803 tig0031918:+41001 None:intergenic
GAGAGAGTCAAGACCCTGCA+CGG 0.620705 tig0031918:+41054 None:intergenic
CCCGACGGTGACGCCAAACG+AGG 0.635086 tig0031918:-40900 Msa1447590:CDS
TCGCTTCGACTCGTAAGAGT+CGG 0.636951 tig0031918:+41234 None:intergenic
GACGATTTAAACCCGAACCT+AGG 0.657672 tig0031918:-40962 Msa1447590:CDS
CGAGCCGGACGAGTTATCAT+CGG 0.665378 tig0031918:+41189 None:intergenic
ATAACCGCCACCATTGTCGT+CGG 0.685944 tig0031918:+40745 None:intergenic
AGAGTCAAGACCCTGCACGG+TGG 0.780619 tig0031918:+41057 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAATGCAAAAATGATACC+AGG - tig0031918:40671-40690 Msa1447590:CDS 30.0%
TCCAATAGATATCCTAGGTT+CGG + tig0031918:41009-41028 None:intergenic 35.0%
AAGCTTCCAATAGATATCCT+AGG + tig0031918:41014-41033 None:intergenic 35.0%
!! TTGATTTAAGCGGGTTCTTT+TGG - tig0031918:41130-41149 Msa1447590:CDS 35.0%
! ATTCGTAACAATGAAGCGTT+TGG - tig0031918:41165-41184 Msa1447590:CDS 35.0%
! AATGAAGCGTTTGGTTTCAT+GGG - tig0031918:41174-41193 Msa1447590:CDS 35.0%
! GAATCGGTTTCAACTTGAAC+GGG + tig0031918:40817-40836 None:intergenic 40.0%
! CGAATCGGTTTCAACTTGAA+CGG + tig0031918:40818-40837 None:intergenic 40.0%
!! AGTTGAAACCGATTCGTATG+AGG - tig0031918:40822-40841 Msa1447590:CDS 40.0%
CTCGTTAACCTCATACGAAT+CGG + tig0031918:40833-40852 None:intergenic 40.0%
TGAAGACGAAATACTTGCTC+CGG - tig0031918:40936-40955 Msa1447590:CDS 40.0%
CCAATAGATATCCTAGGTTC+GGG + tig0031918:41008-41027 None:intergenic 40.0%
! GAAGCTTCTGATGATGAACT+TGG - tig0031918:41027-41046 Msa1447590:CDS 40.0%
! CCAGATGGAGTTGATTTAAG+CGG - tig0031918:41120-41139 Msa1447590:CDS 40.0%
! CAGATGGAGTTGATTTAAGC+GGG - tig0031918:41121-41140 Msa1447590:CDS 40.0%
! CAATGAAGCGTTTGGTTTCA+TGG - tig0031918:41173-41192 Msa1447590:CDS 40.0%
GGCGGTTATGTAACAATTGA+CGG - tig0031918:41225-41244 Msa1447590:CDS 40.0%
!! CTGTTTGATTATGCTGACTC+CGG - tig0031918:41249-41268 Msa1447590:CDS 40.0%
GAAGACGAAATACTTGCTCC+GGG - tig0031918:40937-40956 Msa1447590:CDS 45.0%
ATCGTCAGAGACTGGTACAT+GGG + tig0031918:40980-40999 None:intergenic 45.0%
AATCGTCAGAGACTGGTACA+TGG + tig0031918:40981-41000 None:intergenic 45.0%
GGGTTTAAATCGTCAGAGAC+TGG + tig0031918:40988-41007 None:intergenic 45.0%
GACGATTTAAACCCGAACCT+AGG - tig0031918:40994-41013 Msa1447590:CDS 45.0%
CCCGAACCTAGGATATCTAT+TGG - tig0031918:41005-41024 Msa1447590:CDS 45.0%
! GGCAACTCTTTTTCCTCGTT+TGG + tig0031918:41072-41091 None:intergenic 45.0%
GTTGCCTGAAACCAACGATT+CGG - tig0031918:41086-41105 Msa1447590:CDS 45.0%
TTGCCTGAAACCAACGATTC+GGG - tig0031918:41087-41106 Msa1447590:CDS 45.0%
CCGCTTAAATCAACTCCATC+TGG + tig0031918:41123-41142 None:intergenic 45.0%
ATCGTCACGAACTCGTTTCC+TGG + tig0031918:40692-40711 None:intergenic 50.0%
! TCGCTTCGACTCGTAAGAGT+CGG + tig0031918:40725-40744 None:intergenic 50.0%
GGACGAGTTATCATCGGAAC+CGG + tig0031918:40764-40783 None:intergenic 50.0%
GGTTCCGATGATAACTCGTC+CGG - tig0031918:40763-40782 Msa1447590:CDS 50.0%
AGAAAATGTCACCACCGTGC+AGG - tig0031918:40888-40907 Msa1447590:CDS 50.0%
GAAAATGTCACCACCGTGCA+GGG - tig0031918:40889-40908 Msa1447590:CDS 50.0%
GTCGGGTTCAAATCTTGACC+CGG + tig0031918:40958-40977 None:intergenic 50.0%
TCAGAGACTGGTACATGGGT+CGG + tig0031918:40976-40995 None:intergenic 50.0%
TGAACTTGGTTTACCCCCGA+CGG - tig0031918:41041-41060 Msa1447590:CDS 50.0%
! CTGAAACCAACGATTCGGGT+CGG - tig0031918:41091-41110 Msa1447590:CDS 50.0%
! TGAAACCAACGATTCGGGTC+GGG - tig0031918:41092-41111 Msa1447590:CDS 50.0%
ATAACCGCCACCATTGTCGT+CGG + tig0031918:41214-41233 None:intergenic 50.0%
! CTGACTCCGGTGATCTTTTG+TGG - tig0031918:41262-41281 Msa1447590:CDS 50.0%
! ACTCCGGTGATCTTTTGTGG+AGG - tig0031918:41265-41284 Msa1447590:CDS 50.0%
CGACCTCCACAAAAGATCAC+CGG + tig0031918:41271-41290 None:intergenic 50.0%
! CGGTGATCTTTTGTGGAGGT+CGG - tig0031918:41269-41288 Msa1447590:CDS 50.0%
! CGAGTTCTCCGAGTTGACTC+CGG - tig0031918:40742-40761 Msa1447590:CDS 55.0%
CATCGGAACCGGAGTCAACT+CGG + tig0031918:40753-40772 None:intergenic 55.0%
CGAGCCGGACGAGTTATCAT+CGG + tig0031918:40770-40789 None:intergenic 55.0%
GTCTGAGTCAACACACGAGC+CGG + tig0031918:40785-40804 None:intergenic 55.0%
!! GGCTCGTGTGTTGACTCAGA+CGG - tig0031918:40784-40803 Msa1447590:CDS 55.0%
!! GCTCGTGTGTTGACTCAGAC+GGG - tig0031918:40785-40804 Msa1447590:CDS 55.0%
GAGAGAGTCAAGACCCTGCA+CGG + tig0031918:40905-40924 None:intergenic 55.0%
CAGAGACTGGTACATGGGTC+GGG + tig0031918:40975-40994 None:intergenic 55.0%
!! CGACCCGAATCGTTGGTTTC+AGG + tig0031918:41093-41112 None:intergenic 55.0%
AGAGTCAAGACCCTGCACGG+TGG + tig0031918:40902-40921 None:intergenic 60.0%
TCCTCGTTTGGCGTCACCGT+CGG + tig0031918:41060-41079 None:intergenic 60.0%
! ACCAACGATTCGGGTCGGGT+TGG - tig0031918:41096-41115 Msa1447590:CDS 60.0%
ACCAACCCGACCCGAATCGT+TGG + tig0031918:41100-41119 None:intergenic 60.0%
TCGTTTGGCGTCACCGTCGG+GGG + tig0031918:41057-41076 None:intergenic 65.0%
CTCGTTTGGCGTCACCGTCG+GGG + tig0031918:41058-41077 None:intergenic 65.0%
CCTCGTTTGGCGTCACCGTC+GGG + tig0031918:41059-41078 None:intergenic 65.0%
!! TCGGGTCGGGTTGGTCCAGA+TGG - tig0031918:41105-41124 Msa1447590:CDS 65.0%
GCCACCATTGTCGTCGGCGA+CGG + tig0031918:41208-41227 None:intergenic 65.0%
GTCGCCGACGACAATGGTGG+CGG - tig0031918:41207-41226 Msa1447590:CDS 65.0%
GTGGAGGTCGGAGACGTTGC+AGG - tig0031918:41281-41300 Msa1447590:CDS 65.0%
CCCGACGGTGACGCCAAACG+AGG - tig0031918:41056-41075 Msa1447590:CDS 70.0%
GACGCCGTCGCCGACGACAA+TGG - tig0031918:41201-41220 Msa1447590:CDS 70.0%
GCCGTCGCCGACGACAATGG+TGG - tig0031918:41204-41223 Msa1447590:CDS 70.0%
Chromosome Type Strat End Strand Name
tig0031918 gene 40667 41311 40667 ID=Msa1447590;Name=Msa1447590
tig0031918 mRNA 40667 41311 40667 ID=Msa1447590-mRNA-1;Parent=Msa1447590;Name=Msa1447590-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|214
tig0031918 exon 40667 41311 40667 ID=Msa1447590-mRNA-1:exon:15989;Parent=Msa1447590-mRNA-1
tig0031918 CDS 40667 41311 40667 ID=Msa1447590-mRNA-1:cds;Parent=Msa1447590-mRNA-1
Gene Sequence

>Msa1447590

ATGGAAGAATGCAAAAATGATACCAGGAAACGAGTTCGTGACGATGACTCAGATGCCGACTCTTACGAGTCGAAGCGAGTTCTCCGAGTTGACTCCGGTTCCGATGATAACTCGTCCGGCTCGTGTGTTGACTCAGACGGGTCTGAACCCGTTCAAGTTGAAACCGATTCGTATGAGGTTAACGAGATACAAGACGAGATTTTGAACATTCTCGACGAGACAGAAAATGTCACCACCGTGCAGGGTCTTGACTCTCTCATCAAGAGCTTTGAAGACGAAATACTTGCTCCGGGTCAAGATTTGAACCCGACCCATGTACCAGTCTCTGACGATTTAAACCCGAACCTAGGATATCTATTGGAAGCTTCTGATGATGAACTTGGTTTACCCCCGACGGTGACGCCAAACGAGGAAAAAGAGTTGCCTGAAACCAACGATTCGGGTCGGGTTGGTCCAGATGGAGTTGATTTAAGCGGGTTCTTTTGGTTTGAAGAAGATATTCGTAACAATGAAGCGTTTGGTTTCATGGGTTATGACGCCGTCGCCGACGACAATGGTGGCGGTTATGTAACAATTGACGGACTGTTTGATTATGCTGACTCCGGTGATCTTTTGTGGAGGTCGGAGACGTTGCAGGCTATGTAG
Protein sequence

>Msa1447590

MEECKNDTRKRVRDDDSDADSYESKRVLRVDSGSDDNSSGSCVDSDGSEPVQVETDSYEVNEIQDEILNILDETENVTTVQGLDSLIKSFEDEILAPGQDLNPTHVPVSDDLNPNLGYLLEASDDELGLPPTVTPNEEKELPETNDSGRVGPDGVDLSGFFWFEEDIRNNEAFGFMGYDAVADDNGGGYVTIDGLFDYADSGDLLWRSETLQAM*